Contacts of the strand formed by residues 133 - 141 (chain M) in PDB entry 5DSV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with CYS 133 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30M VAL* 3.8 5.2 - - - -
78M ALA 3.4 14.4 - - - +
80M LEU 3.9 13.7 - - - +
83M ASP* 4.1 6.1 - - - -
84M ALA* 3.5 29.2 - - + -
87M LEU* 3.3 33.4 - - - +
119M VAL* 5.5 1.4 - - - +
131M PHE* 3.3 8.7 + - - +
132M GLY* 1.3 79.2 - - - +
134M SER* 1.3 63.5 + - - +
135M PHE* 4.5 5.9 - - - -
151M ILE 4.4 0.3 - - - +
152M ASP 4.2 1.4 - - - -
153M PRO* 3.6 19.2 - - - +
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Residues in contact with SER 134 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M VAL* 3.4 20.1 - - - +
77M VAL* 3.7 0.7 - - - +
78M ALA 3.0 27.3 + - - +
133M CYS* 1.3 76.4 - - - +
135M PHE* 1.3 65.9 + - - +
150M MET* 4.4 2.1 - - - -
151M ILE 3.2 12.3 - - - -
152M ASP* 3.4 10.5 - - - +
153M PRO* 3.4 17.7 - - - +
165M ILE* 3.9 25.9 - - - +
169M ARG* 4.0 7.4 + - - -
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Residues in contact with PHE 135 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M MET* 3.7 26.9 - - + -
76M ALA 3.1 13.9 - - - +
77M VAL* 3.7 17.7 - - + -
87M LEU* 4.0 27.4 - - + -
91M ALA* 6.1 0.4 - - + -
115M VAL* 3.5 30.1 - - + -
119M VAL* 4.3 2.9 - - + -
133M CYS* 4.5 4.7 - - - -
134M SER* 1.3 80.6 - - - +
136M MET* 1.3 66.9 + - - +
137M LEU* 4.0 19.7 - - + -
150M MET* 3.3 4.7 - - - +
151M ILE* 2.9 79.6 + - + +
165M ILE* 3.9 2.9 - - - -
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Residues in contact with MET 136 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36M ALA 4.5 0.4 - - - +
37M ILE* 4.2 7.4 - - - -
38M GLY* 4.0 21.3 - - - +
47M PHE* 3.8 22.5 - - + -
74M GLY 3.5 0.7 - - - +
75M MET* 3.2 7.1 - - - +
76M ALA* 2.8 40.0 + - - +
135M PHE* 1.3 80.1 - - - +
137M LEU* 1.3 63.7 + - - +
148M LEU* 4.3 10.1 - - + -
149M TYR 2.9 13.5 - - - +
150M MET* 4.0 13.9 - - + -
163M CYS* 3.4 51.6 - - + +
164M ALA* 4.0 0.9 - - - +
165M ILE* 4.0 16.4 - - + -
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Residues in contact with LEU 137 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M PHE* 3.9 2.9 - - - -
69M VAL* 4.5 4.7 - - + -
73M VAL* 4.3 9.6 - - + -
74M GLY 3.2 4.7 - - - +
75M MET* 3.8 33.9 - - + -
91M ALA* 5.3 3.1 - - + -
108M LEU* 3.5 19.0 - - + +
111M LEU* 4.2 17.0 - - + +
112M ALA* 3.9 35.4 - - + +
115M VAL* 5.4 4.3 - - + -
135M PHE* 4.0 23.8 - - + -
136M MET* 1.3 73.7 - - - +
138M GLY* 1.3 58.4 + - - +
148M LEU* 3.4 3.6 - - - +
149M TYR* 2.8 41.5 + - + +
151M ILE* 4.4 3.6 - - + -
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Residues in contact with GLY 138 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M VAL* 4.6 5.2 - - - -
47M PHE* 3.5 18.3 - - - -
72M HIS 3.9 0.5 - - - +
73M VAL* 3.4 1.4 - - - -
74M GLY* 2.8 34.0 + - - -
108M LEU* 3.9 2.7 - - - -
137M LEU* 1.3 74.7 - - - +
139M SER* 1.3 61.2 + - - -
147M GLN 3.3 9.9 - - - -
148M LEU* 4.5 1.3 - - - -
216M VAL* 4.1 9.9 - - - +
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Residues in contact with SER 139 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45M VAL* 3.9 2.4 - - - +
72M HIS* 3.1 34.2 - - - -
73M VAL* 4.2 0.2 - - - -
108M LEU* 3.7 31.7 + - - +
138M GLY* 1.3 74.4 - - - -
140M TYR* 1.3 64.7 + - - +
141M SER 4.7 0.7 + - - -
144M ASP* 6.0 0.7 - - - +
145M GLY 3.9 0.7 + - - +
146M ALA* 3.6 2.6 - - - -
147M GLN* 2.9 39.8 + - - +
216M VAL* 3.8 10.2 - - - +
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Residues in contact with TYR 140 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M LYS 4.7 2.9 - - - -
43M ASP* 3.6 23.1 - - - -
44M GLY* 4.5 2.0 - - - -
72M HIS* 4.0 9.0 + - - +
139M SER* 1.3 78.7 - - - +
141M SER* 1.3 80.9 - - - +
142M VAL* 3.9 23.7 - - + +
145M GLY* 3.4 14.4 - - - -
146M ALA* 3.4 23.1 - - + -
216M VAL* 3.7 7.5 - - + +
217M GLY* 3.5 22.7 - - - +
218M GLU* 3.2 45.5 + - + +
221M ASN 5.9 0.4 - - - -
222M GLY* 3.4 28.0 - - - +
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Residues in contact with SER 141 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72M HIS* 5.7 4.7 - - - -
105M ASN* 5.7 7.2 - - - -
139M SER* 4.4 1.8 + - - -
140M TYR* 1.3 87.8 - - - +
142M VAL* 1.3 60.6 + - - +
143M ASN* 3.8 5.6 + - - +
144M ASP* 3.5 29.1 + - - +
145M GLY* 2.9 31.3 + - - +
221M ASN 6.0 0.2 - - - -
222M GLY* 5.2 2.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il